Literature DB >> 33452285

Evaluation metrics and validation of presence-only species distribution models based on distributional maps with varying coverage.

Kamil Konowalik1, Agata Nosol2.   

Abstract

We examine how different datasets, including georeferenced hardcopy maps of different extents and georeferenced herbarium specimens (spanning the range from 100 to 85,000 km2) influence ecological niche modeling. We check 13 of the available environmental niche modeling algorithms, using 30 metrics to score their validity and evaluate which are useful for the selection of the best model. The validation is made using an independent dataset comprised of presences and absences collected in a range-wide field survey of Carpathian endemic plant Leucanthemum rotundifolium (Compositae). Our analysis of models' predictive performances indicates that almost all datasets may be used for the construction of a species distributional range. Both very local and very general datasets can produce useful predictions, which may be more detailed than the original ranges. Results also highlight the possibility of using the data from manually georeferenced archival sources in reconstructions aimed at establishing species' ecological niches. We discuss possible applications of those data and associated problems. For the evaluation of models, we suggest employing AUC, MAE, and Bias. We show an example of how AUC and MAE may be combined to select the model with the best performance.

Entities:  

Year:  2021        PMID: 33452285      PMCID: PMC7811024          DOI: 10.1038/s41598-020-80062-1

Source DB:  PubMed          Journal:  Sci Rep        ISSN: 2045-2322            Impact factor:   4.379


  16 in total

1.  Harnessing the world's biodiversity data: promise and peril in ecological niche modeling of species distributions.

Authors:  Robert P Anderson
Journal:  Ann N Y Acad Sci       Date:  2012-02-21       Impact factor: 5.691

2.  New developments in museum-based informatics and applications in biodiversity analysis.

Authors:  Catherine H Graham; Simon Ferrier; Falk Huettman; Craig Moritz; A Townsend Peterson
Journal:  Trends Ecol Evol       Date:  2004-09       Impact factor: 17.712

3.  Detecting reticulate relationships among diploid Leucanthemum Mill. (Compositae, Anthemideae) taxa using multilocus species tree reconstruction methods and AFLP fingerprinting.

Authors:  Kamil Konowalik; Florian Wagner; Salvatore Tomasello; Robert Vogt; Christoph Oberprieler
Journal:  Mol Phylogenet Evol       Date:  2015-06-20       Impact factor: 4.286

4.  Bias correction in species distribution models: pooling survey and collection data for multiple species.

Authors:  William Fithian; Jane Elith; Trevor Hastie; David A Keith
Journal:  Methods Ecol Evol       Date:  2014-10-10       Impact factor: 7.781

5.  The interplay of various sources of noise on reliability of species distribution models hinges on ecological specialisation.

Authors:  Alaaeldin Soultan; Kamran Safi
Journal:  PLoS One       Date:  2017-11-13       Impact factor: 3.240

6.  Phylogenetic climatic niche conservatism and evolution of climatic suitability in Neotropical Angraecinae (Vandeae, Orchidaceae) and their closest African relatives.

Authors:  Marta Kolanowska; Elżbieta Grochocka; Kamil Konowalik
Journal:  PeerJ       Date:  2017-05-16       Impact factor: 2.984

7.  SoilGrids1km--global soil information based on automated mapping.

Authors:  Tomislav Hengl; Jorge Mendes de Jesus; Robert A MacMillan; Niels H Batjes; Gerard B M Heuvelink; Eloi Ribeiro; Alessandro Samuel-Rosa; Bas Kempen; Johan G B Leenaars; Markus G Walsh; Maria Ruiperez Gonzalez
Journal:  PLoS One       Date:  2014-08-29       Impact factor: 3.240

8.  A comparison of absolute performance of different correlative and mechanistic species distribution models in an independent area.

Authors:  Farzin Shabani; Lalit Kumar; Mohsen Ahmadi
Journal:  Ecol Evol       Date:  2016-07-27       Impact factor: 2.912

9.  Evaluating Bayesian spatial methods for modelling species distributions with clumped and restricted occurrence data.

Authors:  David W Redding; Tim C D Lucas; Tim M Blackburn; Kate E Jones
Journal:  PLoS One       Date:  2017-11-30       Impact factor: 3.240

10.  Species Distribution Modelling: Contrasting presence-only models with plot abundance data.

Authors:  Vitor H F Gomes; Stéphanie D IJff; Niels Raes; Iêda Leão Amaral; Rafael P Salomão; Luiz de Souza Coelho; Francisca Dionízia de Almeida Matos; Carolina V Castilho; Diogenes de Andrade Lima Filho; Dairon Cárdenas López; Juan Ernesto Guevara; William E Magnusson; Oliver L Phillips; Florian Wittmann; Marcelo de Jesus Veiga Carim; Maria Pires Martins; Mariana Victória Irume; Daniel Sabatier; Jean-François Molino; Olaf S Bánki; José Renan da Silva Guimarães; Nigel C A Pitman; Maria Teresa Fernandez Piedade; Abel Monteagudo Mendoza; Bruno Garcia Luize; Eduardo Martins Venticinque; Evlyn Márcia Moraes de Leão Novo; Percy Núñez Vargas; Thiago Sanna Freire Silva; Angelo Gilberto Manzatto; John Terborgh; Neidiane Farias Costa Reis; Juan Carlos Montero; Katia Regina Casula; Beatriz S Marimon; Ben-Hur Marimon; Euridice N Honorio Coronado; Ted R Feldpausch; Alvaro Duque; Charles Eugene Zartman; Nicolás Castaño Arboleda; Timothy J Killeen; Bonifacio Mostacedo; Rodolfo Vasquez; Jochen Schöngart; Rafael L Assis; Marcelo Brilhante Medeiros; Marcelo Fragomeni Simon; Ana Andrade; William F Laurance; José Luís Camargo; Layon O Demarchi; Susan G W Laurance; Emanuelle de Sousa Farias; Henrique Eduardo Mendonça Nascimento; Juan David Cardenas Revilla; Adriano Quaresma; Flavia R C Costa; Ima Célia Guimarães Vieira; Bruno Barçante Ladvocat Cintra; Hernán Castellanos; Roel Brienen; Pablo R Stevenson; Yuri Feitosa; Joost F Duivenvoorden; Gerardo A Aymard C; Hugo F Mogollón; Natalia Targhetta; James A Comiskey; Alberto Vicentini; Aline Lopes; Gabriel Damasco; Nállarett Dávila; Roosevelt García-Villacorta; Carolina Levis; Juliana Schietti; Priscila Souza; Thaise Emilio; Alfonso Alonso; David Neill; Francisco Dallmeier; Leandro Valle Ferreira; Alejandro Araujo-Murakami; Daniel Praia; Dário Dantas do Amaral; Fernanda Antunes Carvalho; Fernanda Coelho de Souza; Kenneth Feeley; Luzmila Arroyo; Marcelo Petratti Pansonato; Rogerio Gribel; Boris Villa; Juan Carlos Licona; Paul V A Fine; Carlos Cerón; Chris Baraloto; Eliana M Jimenez; Juliana Stropp; Julien Engel; Marcos Silveira; Maria Cristina Peñuela Mora; Pascal Petronelli; Paul Maas; Raquel Thomas-Caesar; Terry W Henkel; Doug Daly; Marcos Ríos Paredes; Tim R Baker; Alfredo Fuentes; Carlos A Peres; Jerome Chave; Jose Luis Marcelo Pena; Kyle G Dexter; Miles R Silman; Peter Møller Jørgensen; Toby Pennington; Anthony Di Fiore; Fernando Cornejo Valverde; Juan Fernando Phillips; Gonzalo Rivas-Torres; Patricio von Hildebrand; Tinde R van Andel; Ademir R Ruschel; Adriana Prieto; Agustín Rudas; Bruce Hoffman; César I A Vela; Edelcilio Marques Barbosa; Egleé L Zent; George Pepe Gallardo Gonzales; Hilda Paulette Dávila Doza; Ires Paula de Andrade Miranda; Jean-Louis Guillaumet; Linder Felipe Mozombite Pinto; Luiz Carlos de Matos Bonates; Natalino Silva; Ricardo Zárate Gómez; Stanford Zent; Therany Gonzales; Vincent A Vos; Yadvinder Malhi; Alexandre A Oliveira; Angela Cano; Bianca Weiss Albuquerque; Corine Vriesendorp; Diego Felipe Correa; Emilio Vilanova Torre; Geertje van der Heijden; Hirma Ramirez-Angulo; José Ferreira Ramos; Kenneth R Young; Maira Rocha; Marcelo Trindade Nascimento; Maria Natalia Umaña Medina; Milton Tirado; Ophelia Wang; Rodrigo Sierra; Armando Torres-Lezama; Casimiro Mendoza; Cid Ferreira; Cláudia Baider; Daniel Villarroel; Henrik Balslev; Italo Mesones; Ligia Estela Urrego Giraldo; Luisa Fernanda Casas; Manuel Augusto Ahuite Reategui; Reynaldo Linares-Palomino; Roderick Zagt; Sasha Cárdenas; William Farfan-Rios; Adeilza Felipe Sampaio; Daniela Pauletto; Elvis H Valderrama Sandoval; Freddy Ramirez Arevalo; Isau Huamantupa-Chuquimaco; Karina Garcia-Cabrera; Lionel Hernandez; Luis Valenzuela Gamarra; Miguel N Alexiades; Susamar Pansini; Walter Palacios Cuenca; William Milliken; Joana Ricardo; Gabriela Lopez-Gonzalez; Edwin Pos; Hans Ter Steege
Journal:  Sci Rep       Date:  2018-01-17       Impact factor: 4.379

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  4 in total

1.  Modeling of Valeriana wallichii Habitat Suitability and Niche Dynamics in the Himalayan Region under Anticipated Climate Change.

Authors:  Priyanka Kumari; Ishfaq Ahmad Wani; Sajid Khan; Susheel Verma; Shazia Mushtaq; Aneela Gulnaz; Bilal Ahamad Paray
Journal:  Biology (Basel)       Date:  2022-03-24

2.  'Fly to a Safer North': Distributional Shifts of the Orchid Ophrys insectifera L. Due to Climate Change.

Authors:  Martha Charitonidou; Konstantinos Kougioumoutzis; Maria Chara Karypidou; John M Halley
Journal:  Biology (Basel)       Date:  2022-03-24

3.  Past climatic refugia and landscape resistance explain spatial genetic structure in Oriental beech in the South Caucasus.

Authors:  Katarzyna Sękiewicz; Irina Danelia; Vahid Farzaliyev; Hamid Gholizadeh; Grzegorz Iszkuło; Alireza Naqinezhad; Elias Ramezani; Peter A Thomas; Dominik Tomaszewski; Łukasz Walas; Monika Dering
Journal:  Ecol Evol       Date:  2022-09-20       Impact factor: 3.167

4.  Phylogeography and colonization pattern of subendemic round-leaved oxeye daisy from the Dinarides to the Carpathians.

Authors:  Kamil Konowalik
Journal:  Sci Rep       Date:  2022-09-30       Impact factor: 4.996

  4 in total

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